Msh4 (mutS homolog 4) - Rat Genome Database

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Gene: Msh4 (mutS homolog 4) Rattus norvegicus
Analyze
Symbol: Msh4
Name: mutS homolog 4
RGD ID: 1309190
Description: Predicted to enable double-stranded DNA binding activity. Predicted to be involved in reciprocal meiotic recombination. Predicted to act upstream of or within several processes, including homologous chromosome pairing at meiosis; ovarian follicle development; and spermatogenesis. Predicted to be located in recombination nodule and synaptonemal complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in primary ovarian insufficiency and spermatogenic failure 2. Orthologous to human MSH4 (mutS homolog 4); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A; dimethylarsinic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC295541; mutS homolog 4 (E. coli); mutS protein homolog 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82245,445,118 - 245,504,493 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2245,452,240 - 245,503,358 (-)EnsemblGRCr8
mRatBN7.22242,785,392 - 242,844,609 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2242,792,661 - 242,843,487 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2250,616,144 - 250,666,160 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02248,509,973 - 248,559,983 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02243,408,533 - 243,458,548 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02260,057,708 - 260,108,897 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2260,057,855 - 260,108,897 (-)Ensemblrn6Rnor6.0
Rnor_5.02278,716,760 - 278,773,060 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42251,801,090 - 251,851,133 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2234,728,057 - 234,775,779 (-)NCBICelera
RGSC_v3.12251,815,109 - 251,866,523 (-)NCBI
Cytogenetic Map2q45NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:10809667   PMID:15467367   PMID:16260499   PMID:18316482   PMID:22164254   PMID:23555294   PMID:27760146  


Genomics

Comparative Map Data
Msh4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82245,445,118 - 245,504,493 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2245,452,240 - 245,503,358 (-)EnsemblGRCr8
mRatBN7.22242,785,392 - 242,844,609 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2242,792,661 - 242,843,487 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2250,616,144 - 250,666,160 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02248,509,973 - 248,559,983 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02243,408,533 - 243,458,548 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02260,057,708 - 260,108,897 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2260,057,855 - 260,108,897 (-)Ensemblrn6Rnor6.0
Rnor_5.02278,716,760 - 278,773,060 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42251,801,090 - 251,851,133 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2234,728,057 - 234,775,779 (-)NCBICelera
RGSC_v3.12251,815,109 - 251,866,523 (-)NCBI
Cytogenetic Map2q45NCBI
MSH4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38175,796,882 - 75,913,242 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl175,796,882 - 75,913,242 (+)Ensemblhg38GRCh38
GRCh37176,262,567 - 76,378,927 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36176,035,218 - 76,151,511 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34175,974,650 - 76,090,944NCBI
Celera174,502,536 - 74,619,128 (+)NCBICelera
Cytogenetic Map1p31.1NCBI
HuRef174,392,386 - 74,509,072 (+)NCBIHuRef
CHM1_1176,377,843 - 76,494,293 (+)NCBICHM1_1
T2T-CHM13v2.0175,633,544 - 75,751,219 (+)NCBIT2T-CHM13v2.0
Msh4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393153,562,783 - 153,611,495 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3153,562,786 - 153,611,775 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm383153,857,141 - 153,906,138 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3153,857,149 - 153,906,138 (-)Ensemblmm10GRCm38
MGSCv373153,520,111 - 153,569,102 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv363153,794,533 - 153,843,524 (-)NCBIMGSCv36mm8
Celera3160,320,812 - 160,369,813 (-)NCBICelera
Cytogenetic Map3H3NCBI
cM Map378.7NCBI
Msh4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542317,093,573 - 17,154,910 (-)Ensembl
ChiLan1.0NW_00495542317,093,573 - 17,154,910 (-)NCBIChiLan1.0ChiLan1.0
MSH4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21150,974,838 - 151,096,427 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11150,135,382 - 150,256,962 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0175,011,947 - 75,130,036 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1176,983,852 - 77,099,896 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl176,983,852 - 77,099,896 (+)EnsemblpanPan2panpan1.1
MSH4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1670,745,777 - 70,822,507 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl670,746,634 - 70,823,004 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha673,406,292 - 73,487,796 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0671,334,444 - 71,416,137 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl671,334,763 - 71,412,508 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1670,834,791 - 70,912,065 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0670,780,166 - 70,856,995 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0671,269,093 - 71,350,596 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Msh4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505887,311,249 - 87,388,210 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365712,822,058 - 2,898,562 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365712,827,283 - 2,898,562 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSH4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12057,283,723 - 57,397,871 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2057,284,575 - 57,396,797 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603360,112,696 - 60,228,261 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Msh4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474221,098,101 - 21,167,398 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474221,098,102 - 21,167,472 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Msh4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v137,738,977 - 7,786,919 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Msh4
648 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:14
Count of miRNA genes:14
Interacting mature miRNAs:14
Transcripts:ENSRNOT00000014106
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2205135267250135267Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2210956252251712708Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2143344967251712708Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2214404877251712708Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2143344967251712708Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2220274283249795005Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2203664411248664411Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2204795005249795005Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2214404877251712708Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2214404877251712708Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2218051934251712708Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2214404877251712708Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2220274283249795005Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660251712708Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2196140964251540988Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2205135267250135267Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2214404877251712708Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2205135267250135267Rat

Markers in Region
RH127932  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr82245,504,684 - 245,504,901 (+)Marker Load Pipeline
mRatBN7.22242,844,856 - 242,845,073 (+)MAPPERmRatBN7.2
Rnor_6.02260,110,408 - 260,110,624NCBIRnor6.0
Rnor_5.02278,774,475 - 278,774,691UniSTSRnor5.0
RGSC_v3.42251,852,644 - 251,852,860UniSTSRGSC3.4
Celera2234,777,290 - 234,777,506UniSTS
RH 3.4 Map21629.8UniSTS
Cytogenetic Map2q45UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
6 3 26 105 38 44 14 76 14 6 186 118 5 94 45 67 30 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000014106   ⟹   ENSRNOP00000014106
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2245,452,240 - 245,503,358 (-)Ensembl
mRatBN7.2 Ensembl2242,792,661 - 242,843,487 (-)Ensembl
Rnor_6.0 Ensembl2260,057,855 - 260,108,897 (-)Ensembl
RefSeq Acc Id: NM_001106477   ⟹   NP_001099947
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82245,452,240 - 245,503,189 (-)NCBI
mRatBN7.22242,792,407 - 242,843,361 (-)NCBI
Rnor_6.02260,057,855 - 260,108,897 (-)NCBI
Rnor_5.02278,716,760 - 278,773,060 (-)NCBI
RGSC_v3.42251,801,090 - 251,851,133 (-)RGD
Celera2234,728,057 - 234,775,779 (-)RGD
Sequence:
RefSeq Acc Id: XM_039102112   ⟹   XP_038958040
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82245,445,118 - 245,504,493 (-)NCBI
mRatBN7.22242,785,392 - 242,844,609 (-)NCBI
RefSeq Acc Id: XM_039102113   ⟹   XP_038958041
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82245,452,744 - 245,486,327 (-)NCBI
mRatBN7.22242,792,772 - 242,826,500 (-)NCBI
RefSeq Acc Id: XM_039102114   ⟹   XP_038958042
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82245,452,744 - 245,476,386 (-)NCBI
mRatBN7.22242,792,772 - 242,816,557 (-)NCBI
RefSeq Acc Id: XM_063281671   ⟹   XP_063137741
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82245,452,744 - 245,486,335 (-)NCBI
RefSeq Acc Id: XR_010063597
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82245,452,997 - 245,504,493 (-)NCBI
RefSeq Acc Id: NP_001099947   ⟸   NM_001106477
- UniProtKB: F1M9U4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000014106   ⟸   ENSRNOT00000014106
RefSeq Acc Id: XP_038958040   ⟸   XM_039102112
- Peptide Label: isoform X1
- UniProtKB: F1M9U4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038958041   ⟸   XM_039102113
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038958042   ⟸   XM_039102114
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063137741   ⟸   XM_063281671
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M9U4-F1-model_v2 AlphaFold F1M9U4 1-911 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309190 AgrOrtholog
BioCyc Gene G2FUF-50777 BioCyc
Ensembl Genes ENSRNOG00000010431 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014106 ENTREZGENE
  ENSRNOT00000014106.7 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1420.10 UniProtKB/TrEMBL
  3.30.420.110 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
InterPro DNA_mismatch_repair_MutS_C UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_clamp UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_core UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_sf UniProtKB/TrEMBL
  DNA_mmatch_repair_MutS_con_dom UniProtKB/TrEMBL
  MutS_con_dom_sf UniProtKB/TrEMBL
  MutS_family UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
NCBI Gene 295541 ENTREZGENE
PANTHER MUTS PROTEIN HOMOLOG 4 UniProtKB/TrEMBL
  PTHR11361 UniProtKB/TrEMBL
Pfam MutS_II UniProtKB/TrEMBL
  MutS_III UniProtKB/TrEMBL
  MutS_IV UniProtKB/TrEMBL
  MutS_V UniProtKB/TrEMBL
PhenoGen Msh4 PhenoGen
PROSITE DNA_MISMATCH_REPAIR_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000010431 RatGTEx
SMART MUTSac UniProtKB/TrEMBL
  MUTSd UniProtKB/TrEMBL
Superfamily-SCOP DNA_mismatch_repair_MutS_connt UniProtKB/TrEMBL
  DNA_repair_MutS_domIII UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt F1M9U4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-19 Msh4  mutS homolog 4  Msh4  mutS homolog 4 (E. coli)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Msh4  mutS homolog 4 (E. coli)   Msh4_predicted  mutS homolog 4 (E. coli) (predicted)  'predicted' is removed 2292626 APPROVED
2008-01-09 Msh4_predicted  mutS homolog 4 (E. coli) (predicted)  LOC688159  similar to mutS homolog 4  Data merged from RGD:1592401 1643240 APPROVED
2006-11-20 LOC688159  similar to mutS homolog 4      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Msh4_predicted  mutS homolog 4 (E. coli) (predicted)      Symbol and Name status set to approved 70820 APPROVED